The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document


Variant: NM_001354803.2:c.295del

CA2018007672

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 0c341913-df27-4583-812e-f7e5e0c9d34a

HGVS expressions

NM_001354803.2:c.295del
NC_000007.14:g.44145274del
CM000669.2:g.44145274del
NC_000007.13:g.44184873del
CM000669.1:g.44184873del
NC_000007.12:g.44151398del
NG_008847.1:g.49151del
NG_008847.2:g.57898del
ENST00000395796.8:c.*1259del
ENST00000616242.5:c.*381del
ENST00000683378.1:n.487del
ENST00000336642.9:c.295del
ENST00000345378.7:c.1264del
ENST00000403799.8:c.1261del
ENST00000671824.1:c.1324del
ENST00000672743.1:n.273del
ENST00000673284.1:c.1261del
ENST00000336642.8:n.313del
ENST00000345378.6:c.1264del
ENST00000395796.7:c.1258del
ENST00000403799.7:c.1261del
ENST00000437084.1:c.1210del
ENST00000459642.1:n.641del
ENST00000616242.4:n.1258del
NM_000162.3:c.1261del
NM_033507.1:c.1264del
NM_033508.1:c.1258del
NM_000162.4:c.1261del
NM_001354800.1:c.1261del
NM_001354801.1:c.250del
NM_001354802.1:c.121del
NM_001354803.1:c.295del
NM_033507.2:c.1264del
NM_033508.2:c.1258del
NM_000162.5:c.1261del
NM_033507.3:c.1264del
NM_033508.3:c.1258del

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GCK Version 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1261del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 421 (NM_000162.5), adding 10 novel amino acids before encountering a stop codon (p.(Glu421SerfsTer10)). While this variant, located in exon 10 of 10, is predicted to cause a premature stop codon and to escape nonsense mediated decay, it is in a functionally important region of a gene where loss-of-function is an established disease mechanism (PVS1). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in one individual with non-autoimmune or non-absolute/near-absolute insulin-deficient diabetes/hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID 16965331). However, the clinical history for this individual is highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; PMID: 16965331). Taken together, this evidence supports the classification of this variant as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2, approved 6/7/2023: PVS1, PM2_Supporting, PP4.
Met criteria codes
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting)
PVS1
While this variant, located in exon 10 of 10, is predicted to cause a premature stop codon and to escape nonsense mediated decay, it is in a functionally important region of a gene where loss-of-function is an established disease mechanism (PVS1)
PP4
This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; PMID: 16965331).
Not Met criteria codes
PS4
This variant was identified in one individual who does not have autoimmune or absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID 16965331).
Approved on: 2023-06-26
Published on: 2023-06-26
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